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Network Construction, NetSynthesis

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Encyclopedia of Systems Biology

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Definition

A biological network refers to the representation of relationships among various types of biological entities. Each node in the network refers to a biological entity and a pair of related entities is connected with an edge in the network. An example of a biological network is a protein–protein interaction network, in which the nodes are the proteins and a pair of proteins connected with an edge corresponds to an interaction between the protein pair. NetSynthesis is a method to build such kind of biological networks by means of text-mining queries over Medline abstracts.

Characteristics

While interaction data from manually curated databases are highly useful as a concise resource for biologists, the level of detail about the interactions is a priori defined by the databases. The interactions are often restricted to specific kinds of information so that information one might be interested, such as the structure or strength of the interactions, might not be captured in the...

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References

  • Grinberg D, Lafferty J, Sleator D (1995) A Robust Parsing Algorithm For Link Grammars. CMU-CS-TR-95-125

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  • Tari L, Hakenberg J, Gonzalez G, Baral C (2009) Querying parse tree database of Medline text to synthesize user-specific biomolecular networks. Pac Symp Biocomput 14:87–98

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  • Tari L, Tu PH, Hakenberg J, Chen Y, Son TC, Gonzalez G, Baral C (2010) Incremental Information Extraction Using Relational Databases. IEEE Trans Knowl Data Eng 99

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Author information

Authors and Affiliations

  1. Pharma Early Development Informatics, Hoffmann-La Roche Inc., 340 Kingsland St, Nutley, NJ, 07110-1199, USA

    Dr. Luis Tari

Authors
  1. Dr. Luis Tari
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Corresponding author

Correspondence to Luis Tari .

Editor information

Editors and Affiliations

  1. Biomedical Sciences Research Institute, University of Ulster, Coleraine, UK

    Werner Dubitzky

  2. Department of Computer Science, University of Rostock, Rostock, Germany

    Olaf Wolkenhauer

  3. Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea

    Kwang-Hyun Cho

  4. Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA

    Hiroki Yokota

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Tari, L. (2013). Network Construction, NetSynthesis. In: Dubitzky, W., Wolkenhauer, O., Cho, KH., Yokota, H. (eds) Encyclopedia of Systems Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-9863-7_159

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